ME/CFS for 2/3 of their life, then multiple COVID


I think my case is unique and interesting.  I have had CFS/ME for 37 years since age 15, but I have been very functional for the most part.  I had been worsening over the past 8-10 years and discovered high mold levels 3 years ago in my house.  I developed MCAS and related symptoms from the mold.  But with treatment I was improving ( See Pre-COVID Thryve sample which is quite good.)

Then contracted COVID in Nov 2021.  I had a moderately severe acute COVID illness and did not recover fully, developed Long COVID.  Shortness of breath, low o2 sat, palpitations,  dysautonomia, insomnia, irritable bladder, cognitive issues much worse than CFS/ME. My GI issues were not too bad though.  Diarrhea on and off for several weeks.  Gas and bloating that aligned with my MCAS fluctuations.  I did have a GI Effects test done during this time (Feb 2022) and it wasn’t too bad (5 score on dysbiosis 0 or 1 on other markers, 2 on inflammation.  I know the limitations of that test. 

My health steadily improved and as of 2 months ago I was 85% from my pre-COVID health.  But contracted respiratory illness, most likely COVID again.  Sore throat, congestion, GI issues.  Took 3 weeks to resolve sore throat and congestion but GI issues have worsened over the last 5 weeks.  Alternate between diarrhea and constipation, gas, cramping, MCAS worse.  Passed out earlier this week when experiencing cramping.  Had strange derealization experience at that time, kind of like a flashback or deja vu.  Fatigue and cognitive issues are getting worse as well.  


My tell-tale test for ME/CFS and Long COVID is massive over-representation of the 0-9%ile. The number in each percentile range should be around the same in a normal microbiome. These are often different from patient to patient. For other ME/CFS or Long COVID analysis, see this page.

0 – 95172
10 – 191218
20 – 291818
30 – 391418
40 – 491620
50 – 591920
60 – 691319
70 – 792618
80 – 891718
90 – 991722

Looking at Dr. Jason Hawrelak Recommendations, we see a lot of items out of position.

TaxonomyRankLowHighYour ValueStatusHand Pick
Bacteroidiaclass03537.085Not Ideal
Akkermansiagenus130.354Not Ideal
Bacteroidesgenus02031.372Not Ideal
Bifidobacteriumgenus2.550.005Not Ideal
Blautiagenus51011.271Not Ideal
Lactobacillusgenus0.0110.006Not Ideal
Methanobrevibactergenus0.00010.020Not Ideal
Roseburiagenus5100.472Not Ideal
Proteobacteriaphylum048.94Not Ideal
Bilophila wadsworthiaspecies00.250.093Ideal
Escherichia colispecies00.010Ideal
Faecalibacterium prausnitziispecies10152.902Not Ideal
Overall Percentile Ranking56.5% 

One item to note is Bifidobacterium which appears to be associated to allergies and potentially MCS (see Mast Cells and Bifidobacteria)

The Bacteria deemed Unhealthy list had some interesting items:

  • Rickettsia at 99%ile and Ehrlichia at 96%ile — this genus was the focus of Dr. Cecile Jadin work with ME/CFS over the last 3 decades. I recently did another post on these High Tick-borne Bacteria Counts (P.S. Dr. Jadin is working on a draft of her current protocol for this site — stay tune)
  • Faecalibacterium prausnitzii species at 17%ile, Reduced Ability to handle inflammation

As with another person who had ME/CFS and then Long COVID, let us look at the matches to published literature:

  •  Long COVID   (62 %ile) 14 of 204
  •  COVID-19   (59 %ile) 11 of 118
  •  Chronic Fatigue Syndrome   (60 %ile) 4 of 64
  •  Irritable Bowel Syndrome   (80 %ile) 10 of 68
  •  Allergic Rhinitis (Hay Fever)   (98 %ile) 6 of 39

Other matches were interesting, Insomnia   (0 %ile) 0 of 26, which implies that sleep issues are likely atypical. These are very rough estimates (the studies were done with different lab processes, so the data is fuzzy).

Going Forward

I started with the “Just give me Suggestions” and then manually did the 5 items above. Why? To give emphasis to the likely bacteria that may be of main concerns. So we see:

The highest (and lowest) priority were 466 and -453. So our emphasis would be items over 233 and below 227 to give us the best odds. Yes, odds — everything is done by fuzzy logic and probability.

The top easy to do items are:

Flipping over to the other side, items to reduce or avoid if possible:

I have often suggested barley or oats porridge with walnuts for breakfast each day — that provides lots of fiber. As for milk with it– Yakult — which contains lactobacillus casei (probiotics). And cacoa / chocolate — see Honestly! Chocolate!!! [2012], Bifidobacterium, Chocolate and CFS [2014] and Chocolate & Blueberries– Good Medicine for Bifidobacteria [2017]. All of the following are positives: blueberry, whole-grain barley, oats and barley,oat.

Going over to Retail probiotics, see several safe(no adverse impact detected) one including: symbiopharm / symbioflo 2, enterogermina and Filmjölk (SE) / Filmjölk (hard to get outside of Sweden).

Flipping over to Food Menu Planner we see a short list of high priority items. The top one: inulin and fiber cited above are a convergence… but what about the other oddities?

👍61.111,4-Naphtoquinone — in Walnuts Liquor
👍53.01Isoferulic acid — vinegar
👍43.39Raffinose — in
Artichoke, jerusalem, peeled, boiled, drained
(which is also used for inulin)
👍34.1302 mersChocolate, dark
👍31.71OligosaccharidesPea, split, dried (or supplements)
👍30.22Apigenin 7-O-glucuronideGlobe artichoke, heads, raw

As a reminder, many studies use the above nutrients (and the food it comes from may not have been studied). The Food Menu attempt to resolve this disconnect. So Artichokes of different types should be regularly on your supper menu — perhaps with pea soup or just boiled peas.


My current diet (low carb, higher saturated fat, high red meat) is a poor choice according to these results.  The low carb approach works well for my blood sugar and for keeping my weight down, but I do crave good carbs.  I eat a lot of vegetables but it is impossible to get enough fiber that way.  I had been supplementing with a rotation of psyllium, flax and chia. I will slowly adjust my diet to a higher carb, lower fat one and see how I respond.  I have done well with oats in the past. I think as long as I combine the starches with lean protein I will do fine. 

I used inulin during my first Covid infection and seemed to do well with it.

With regard to probiotics, bacillus subtilis looks to be a great choice, but different strains are used in the studies and most are not available commercially.  The one commercially available  microbiome labs /hu58 is marginally “likely safe”. 

I am going to try Yakult.  What would be your second choice? 

Nicotine is interesting.  This was talked about early on as being protected for Covid.  Now it is gaining popularity as many are trying for Long Covid.

It is disappointing there are no strong consensus herbs or spices.  


A: Concerning Probiotics, there is a second approach — looking at the genes you have in your bacteria and what they are not producing enough of.

The top 1 is Escherichia coli — available in two products: Mutaflor and Symbioflor-2. The next ones that are relatively easy to obtain are Bacillus subtilis and a specific species: Bacillus subtilis subsp. natto. This later item is available in many Japanese food sections of some grocery stores. It is just called Natto. It is made using soy which is also on your positive list. It also is a fibrinolytic (unthickens thick blood).

Q: “Should I consider rosemary stronger because of ursolic acid?”

A: No, the numbers indicated confidence of the item having a positive or negative effect. They are not “better” or “stronger” numbers, just more likely to have some effect (may be minor). We are using fuzzy logic, hence odds and the odds are on causing shifts and NOT the amount of shift. That is all that we can get from the studies usually.
Bacillus subtilis subsp. natto

Bottom Line

This microbiome matches the pattern for ME/CFS and Long COVID. Most of the suggests have been studied with ME/CFS with positive results. Now it is just a matter of doing. After 6-10 weeks do another microbiome sample so you may make the next course adjustment. Most people cascade into ME/CFS, getting out is a dog-legged journey.

Addendum Exploration

I decided to look how the indices change with age. As you can see below, in general they decrease or increase significantly with age as I would expect. For more information see this earlier post.


Symptom NameShannonSimpsonChaoShannon
Age: 0-101.5760.118878833.165.244.821
Age: 20-301.5990.0651159232.249.752.657
Age: 30-401.5790.061111931.943.552.9153
Age: 40-501.620.0671043334.847.150.5106
Age: 50-601.6050.0451172832.834.155.347
Age: 60-701.4880.03313580282660.722

Alpha Diversity Indices:

For a general introduction.. Personally, they are unlikely to be useful in an individual context and are complex to fully understand. I include this as an exploration

  1. Shannon Diversity Index: 1.39 / 16.3%ile
    • Closest to: Comorbid: Salicylate sensitive;Other: Sensitivity to vibrations;Neurological-Vision: Blurred Vision;DePaul University Fatigue Questionnaire : Tingling feeling;DePaul University Fatigue Questionnaire : Blurred Vision;Immune Manifestations: Thick blood / Hypercoagulation
  2. Simpson Diversity Index: 0.04 / 31.2%ile
    • Closest to: Age: 60-70; Neurological: fasciculations; Other: Sensitivity to vibrations
  3. Chao1 Index :16371 / 76.6%ile
    • Closest to: DePaul University Fatigue Questionnaire : Does physical activity make you feel better; Age: 60-70; Comorbid: Restless Leg; Onset: less than 08 years since onset; DePaul University Fatigue Questionnaire : Chemical sensitivity

Symptoms versus Alpha Diversity Indices

I recently exposed the Diversity Indices to all users on Microbiome Prescription. It is on the [Research Features] tab.

I then computed the average and also the average percentile for each symptom. I prefer to use percentile because the distribution is not a bell curve. Converting to percentiles transform it to a uniform distribution which is easier to work with for statistical tests. Percentiles are also easier for people to understand.

See this write up by CosmosId to explain these indices. I also attach the data as a CSV file for those who want to play with sorting the data in different manners. For all of the Rank, 50 is what would be expected from a general healthy population.

These Measures are Age And Lab Sensitive

Symptom NameShannonSimpsonChaoShannon
Age: 0-101.5760.118878833.165.244.821
Age: 20-301.5990.0651159232.249.752.657
Age: 30-401.5790.061111931.943.552.9153
Age: 40-501.620.0671043334.847.150.5106
Age: 50-601.6050.0451172832.834.155.347
Age: 60-701.4880.03313580282660.722
SymptomNameShannonSimpsonchaoShannon RankSimpson RankChao Rankobservations
Age: 20-302.180.0623606549.615.238
Age: 30-402.1160.06205861.650.313.969
Age: 40-501.8480.071172447.853.911.753
Age: 50-601.7470.039201942.832.513.947
Age: 60-701.9260.058169152.143.711.475
Symptom NameShannonSimpsonchaoShannon RankSimpson RankChao Rankobservations
Age: 0-102.2930.1341979764.167.769.852
Age: 20-302.6160.1032154974.863.269.131
Age: 30-402.8160.0831639481.763.467.296
Age: 40-502.890.092027584.862.274.153
Age: 50-603.0250.0762195686.65475.938
Age: 60-702.5960.0772774072.45172.672
Ombre/Thryve Data

For anyone wishing to dig further, all of the raw data is on our citizen science site for download. For example, you can compute lab specific percentiles for each symptom.

Symptom NameShannonSimpsonChaoShannon RankSimpson RankChao RankObs
Asymptomatic: Minor Health Issues (a few symptoms only)1.9310.0484856.98350.740.52658
Official Diagnosis: Ulcerative colitis1.7050.085547.47835.254.727.523
Neurological: Spatial instability and disorientation2.0490.0725981.80455.251.829.556
Asymptomatic: No Health Issues2.0120.0668924.89953.745.429.6188
Joint: Sudden and severe episodes of pain2.1850.0586160.83358.548.530.648
Neuroendocrine: Feeling like you have a high temperature1.9670.0756704.37350.953.832.675
Autonomic: Blurred or tunnel vision after standing1.9070.0546777.78449.942.133.251
Neuroendocrine Manifestations: abnormal appetite2.0120.067345.45553.244.834.177
Neurological: fasciculations1.8630.0558333.947.943.334.270
Onset: over 31 years since onset1.6570.0897253.21938.747.234.632
Neurological: Confusion1.9180.0677627.78549.448.43593
Immune Manifestations: Diarrhea1.9360.07512798.5748.952.435178
Neuroendocrine: Feeling like you have a low temperature1.9630.0697193.58351.54835.360
Neurological-Vision: Blurred Vision1.8670.0597616.11946.44435.4151
Autonomic: Graying or blacking out after standing2.0370.0587603.08655.945.335.535
Neuroendocrine: Chills or shivers1.8130.0837818.41145.252.635.656
Neuroendocrine Manifestations: recurrent feelings of feverishness1.9750.0598146.89251.24836.265
Neurological: Difficulty processing information (Understanding)1.90.0718249.88348.348.136.3197
Neuroendocrine Manifestations: Neuralgia1.910.06710588.1447.249.636.444
Neurological-Sleep: Chaotic diurnal sleep rhythms (Erratic Sleep)2.0090.05911433.4551.643.436.5231
Neuroendocrine: Temperature fluctuations throughout the day1.9570.0657482.10349.850.336.568
Neurological: Impairment of concentration1.9810.05910024.1251.643.836.8345
Immune Manifestations: tender lymph nodes1.9810.0578632.26451.643.236.9110
Sleep: Sleeping all day and staying awake all night2.070.0747632.56356.354.337.132
Autonomic: Nausea1.9110.078689.97648.851.737.185
Neurological: Short-term memory issues2.0010.0628048.83252.545.637.2220
Neurological: Neuropathy1.9260.05111019.7648.241.437.571
Official Diagnosis: Metabolic Syndrome1.7480.0678212.52443.344.137.621
DePaul University Fatigue Questionnaire : Fever & Chills1.7280.1029503.59140.556.237.622
Neuroendocrine: Lack of appetite1.9460.0649142.98450.544.537.661
Neurological: Executive Decision Making (Difficulty making)2.0060.06111185.7652.444.437.7289
Immune: Sensitivity to smell/food/medication/chemicals1.9790.0679401.0775047.437.8194
Immune Manifestations: Genitorinary / Nocturia – Urinary issues2.0850.077840.6085651.737.851
Neurological: emotional overload2.0650.0668548.66854.849.537.8196
Neuroendocrine Manifestations: Muscle weakness1.950.0628751.74149.646.237.9216
General: Myalgia (pain)2.0090.05913779.452.446.337.9216
Onset: 2000-20101.9490.0648244.57449.847.338122
Neuroendocrine: Lost or gained weight without trying1.9930.078316.81451.650.738.2118
Immune Manifestations: new food sensitivities1.9830.0679932.41450.647.738.2157
Onset: Gradual2.0430.06213699.925547.638.2172
Neurological: High degree of Empathy before onset1.9750.078434.4655151.138.386
Comorbid-Mouth: Dry Mouth1.8560.0558600.48445.741.338.4124
Neuroendocrine Manifestations: subnormal body temperature1.9990.05712240.3452.140.838.4235
Neurological-Vision: Acquired or exertional dyslexia1.9110.0768275.38149.754.138.521
Neuroendocrine Manifestations: Dry Eye (Sicca or Sjogren Syndrome)1.8730.05610422.6645.742.438.5136
Neurocognitive: Slowness of thought1.9580.06112656.6150.644.938.6361
Neuroendocrine: Sweating hands1.910.0918249.43848.256.638.748
Pain: Chest pain2.1240.06910019.4158.352.338.754
Blood Type: B Positive1.7530.0858271.44440.455.838.736
Neurological-Vision: inability to focus eye/vision1.9460.06112655.2249.642.138.8224
Neurological: Difficulty reading1.9660.06611904.1350.545.139283
Neurological-Vision: Impaired Depth Perceptions1.9170.0939048.09146.349.73933
Asymptomatic: Live in house with person with probable microbiome dysfunction1.9540.0579649.83150.143.23971
Neurocognitive: Absent-mindedness or forgetfulness1.9890.06412091.8151.545.639389
Pain: Pain or aching in muscles1.9580.06812992.849.751.139182
Comorbid: Raynaud’s syndrome (Skin discoloration)1.9170.05215270.644844.73933
Autonomic Manifestations: cardiac arrhythmias1.9550.0549592.80351.440.83961
Pain: Myofascial pain2.0090.06419489.555347.839.189
Neuroendocrine Manifestations: Excessive adrenaline2.0270.0648756.42353.650.539.178
Official Diagnosis: Inflammatory Bowel Disease (IBD)1.9060.0938392.80647.658.539.231
Pain: Joint pain2.0030.06610602.5151.950.639.3178
Joint: Stiffness and swelling2.0410.05912655.6153.14339.3246
Neurological-Sleep: Vivid Dreams/Nightmares2.060.0589058.6754.645.439.3100
Infection: Mycoplasma2.0540.07511920.39545439.4111
Neurological: Disorientation2.1020.0778725.1556.95539.580
Comorbid-Mouth: Gingivits / Gum Disease2.040.068021.0655.747.739.867
Autonomic Manifestations: Cortisol disorders or irregularity2.0150.0648834.63951.847.639.897
General: Headaches1.9910.0612468.851.244.839.9309
Official Diagnosis: Mast Cell Dysfunction2.0120.0613066.2851.843.139.9208
Autonomic: Dizziness or fainting1.9320.0628867.45549.645.539.9112
Immune Manifestations: general malaise1.9620.06113005.8850.544.940339
Comorbid: Hypothyroidism1.9820.06112229.7250.943.540258
Autonomic Manifestations: nausea1.8620.0679328.00946.547.940.1108
Age: 60-701.9970.05714128.2651.240.140.2195
Neuroendocrine Manifestations: Rapid muscular fatiguability2.0240.0639405.63653.446.740.2165
Pain: Aching of the eyes or behind the eyes1.9540.05811520.9349.644.740.398
Immune Manifestations: Alcohol Intolerant1.9670.05912012.2849.941.840.5303
Neurocognitive: Difficulty understanding things1.9420.0719540.41349.849.640.5189
Neurological-Vision: photophobia (Light Sensitivity)2.0040.06312593.7451.244.740.5276
Onset: less than 16 years since onset1.9540.0578948.20549.746.340.783
Autonomic Manifestations: irritable bowel syndrome1.9630.06313226.950.844.240.8378
Neurocognitive: Feeling disoriented1.9760.0659168.40550.849.340.8126
Comorbid-Mouth: TMJ / Dysfunction of the temporomandibular joint syndrome1.9860.05713336.8250.940.240.8223
Autonomic Manifestations: palpitations1.8760.0649256.6544745.940.9133
Infection: Human Herpesvirus 6 (HHV6)2.0560.06814020.1554.249.540.9149
Neuroendocrine Manifestations: worsening of symptoms with stress.1.9890.06110591.7251.144.940.9414
Autonomic Manifestations: Postural orthostatic tachycardia syndrome (POTS)1.9270.0679603.28948.845.240.9128
Onset: less than 04 years since onset2.0340.0738956.18354.153.240.971
Immune Manifestations: Abdominal Pain1.9470.06814265.7649.446.541.1326
Neurological: Word-finding problems2.0570.06410858.3953.546.941.2289
Neurological-Audio: hypersensitivity to noise1.9580.06411562.5349.745.741.2347
Immune Manifestations: recurrent flu-like symptoms2.0010.06615145.9651.848.441.2124
Neuroendocrine: Alcohol intolerance1.9510.0613204.9449.641.841.3278
Post-exertional malaise: Rapid muscular fatigability,2.0240.069815.64552.844.141.4169
Neurocognitive: Problems remembering things1.990.06511390.8151.346.941.4415
Comorbid: Constipation and Explosions (not diarrohea)2.0140.06214823.4752.241.941.5170
Neuroendocrine Manifestations: intolerance of extremes of heat and cold1.9870.0649946.11250.947.341.5249
Pain: Eye pain1.9780.04614356.535137.841.557
Neurological-Audio: Tinnitus (ringing in ear)1.960.06113969.8549.544.841.5392
Blood Type: A Negative1.870.06884547.942.941.524
Neurocognitive: Unable to focus vision and/or attention2.010.06512425.265245.741.6302
Other: Sensitivity to mold2.0430.0679442.87253.550.541.7141
Neurocognitive: Can only focus on one thing at a time1.9810.0611138.7150.74541.7394
Neurological: Cognitive/Sensory Overload1.9880.06710058.0150.749.441.7219
Immune Manifestations: medication sensitivities.2.0920.06113364.0655.544.541.7142
Neurocognitive: Difficulty paying attention for a long period of time2.0020.06411330.785246.841.8429
Immune Manifestations: hives1.9730.05610904.2850.238.641.946
Onset: Sudden1.7040.0688797.21439.947.741.970
Autonomic Manifestations: exertional dyspnea1.7710.0619788.97845.339.94246
Comorbid: Mold Sensitivity / Exposure2.0720.0669522.61354.249.742.1137
Sleep: Need to nap daily1.9550.0619768.21749.746.342.1129
Neuroendocrine Manifestations: sweating episodes2.0740.07113323.8354.647.942.1183
Post-exertional malaise: Inappropriate loss of physical and mental stamina,2.0340.0639683.47852.746.742.1255
Autonomic Manifestations: urinary frequency dysfunction2.0230.078986.06253.649.542.2113
Neurocognitive: Difficulty expressing thoughts1.9960.07410247.5751.849.442.2232
General: Fatigue1.9710.05812031.4650.644.542.3554
Immune: Flu-like symptoms2.0320.06717995.0153.247.342.3116
Neuroendocrine Manifestations: marked weight change2.1150.06913678.2355.350.242.3119
Comorbid-Mouth: Bruxism – Jaw cleanching / Teeth grinding2.0050.06213571.2951.643.242.3318
Neuroendocrine: Feeling hot or cold for no reason1.9850.06710345.5650.548.542.4158
Autonomic: Ocassional Tachycardia (Rapid heart beat)1.9080.0679478.57948.149.242.4121
Gender: Female20.0559736.42751.343.342.4372
Immune: Recurrent Sore throat1.9610.06311439.6749.545.942.5134
Neurological-Sleep: Sleep Apnea2.1480.06619898.158.252.342.6103
Comorbid: Snoring (NOT Sleep Apnea2.0310.05914436.9152.741.642.6185
Sleep: Waking up early in the morning (e.g. 3 AM)2.0570.06212919.9553.34542.7349
Neuroendocrine Manifestations: marked diurnal fluctuation2.1150.0610086.795845.642.724
Immune Manifestations: Mucus in the stool2.0450.07814352.7452.951.642.7176
Neuroendocrine Manifestations: cold extremities1.9610.06114395.249.645.342.8267
Neuroendocrine Manifestations: loss of adaptability1.9630.06522154.925147.442.962
Neurological-Sleep: Night Sweats2.0710.06513304.8853.346.342.9141
Pain: Sensitivity to pain2.0490.07212457.7453.151.142.9181
Immune Manifestations: Bloating1.9770.06313344.0950.34542.9504
Post-exertional malaise: Difficulty reading after mild physical or mental activity1.9910.06510766.6351.24742.9192
Onset: less than 08 years since onset2.0540.0599535.96654.943.34358
Neurological-Sleep: Insomnia2.030.06114473.1752.344.643339
Neuroendocrine: Cold limbs (e.g. arms, legs hands)1.9690.06712977.4950.646.443191
Sleep: Unrefreshed sleep1.9890.05912300.4551.344.143479
Immune Manifestations: Constipation2.0040.05914280.1352.143.243395
General: Depression2.110.06712559.0255.749.143278
Official Diagnosis: Irritable Bowel Syndrome1.9990.06514433.0751.34543.1349
Comorbid: Multiple Chemical Sensitivity2.0530.05612104.9953.941.343.1131
Neuroendocrine Manifestations: Air Hunger1.9310.0589873.46948.844.543.181
Sleep: Daytime drowsiness2.0180.06514393.7352.246.643.1349
Autonomic: Shortness of breath1.9760.0679794.89550.547.843.1124
Immune Manifestations: Thick blood / Hypercoagulation1.990.0619581.98551.246.843.266
Sleep: Problems falling asleep2.0310.06510621.4452.447.843.2221
Infection: Lyme2.0290.05711234.8952.646.843.271
Neurological-Sleep: Inability for deep (delta) sleep2.0970.07114421.5855.948.943.2151
Onset: less than 02 years since onset1.8960.0639318.65746.146.343.367
Onset: 2010-20201.990.06412458.2450.444.743.4325
Age: 10-202.0140.0719357.47553.249.843.440
Autonomic Manifestations: light-headedness1.9880.0710053.8250.449.343.6145
Sleep: Problems staying asleep2.0510.05913891.4952.944.143.7380
Autonomic: Irregular heartbeats2.0470.06814841.5152.84843.8141
Comorbid: Histamine or Mast Cell issues1.9690.05913247.9449.743.543.8355
Other: Sensitivity to vibrations1.9290.04412403.7347.937.343.952
Post-exertional malaise: Mentally tired after the slightest effort2.0180.06310731.3451.547.243.9161
Official Diagnosis: Allergic Rhinitis (Hay Fever)1.9650.05713655.9849.741.643.9232
Infection: Epstein-Barr virus2.1170.0613402.1355.845.444240
Infection: Coxsackie2.10.0619782.61557.347.644.239
Post-exertional malaise: Rapid cognitive fatigability,2.0550.06110488.1953.646.844.2212
Neurocognitive: Brain Fog1.9820.06412153.5850.446.344.3597
Comorbid: Small intestinal bacterial overgrowth (SIBO)2.020.07113923.3151.252.744.4191
Immune: Tender / sore lymph nodes2.0960.06814842.8553.646.744.4111
Post-exertional malaise: Worsening of symptoms after mild mental activity2.0160.07110902.0251.951.444.4165
General: Sinus issues with headaches2.0240.06513296.415246.444.5124
Age: 20-301.9740.0716286.0751.150.944.5136
Post-exertional malaise: Next-day soreness after everyday activities2.1040.06412530.6854.447.244.5198
Immune Manifestations: Inflammation of skin, eyes or joints2.0970.06816251.5554.851.144.6228
Post-exertional malaise: General2.0530.06313379.2153.448.944.6243
Neurological: Slowed speech2.1790.0814630.1157.949.444.7108
Post-exertional malaise: Post-exertional malaise2.0720.0610683.7253.846.344.7269
Neurological: Joint hypermobility2.0630.07215030.9953.348.844.8167
Neurological: Seasonal Affective Disorder (SAD)2.1710.07312976.1858.749.844.9127
Neuroendocrine Manifestations: Laboured breathing2.0030.07711266.0752.151.844.930
Autonomic Manifestations: delayed postural hypotension2.0910.0810730.3256.351.344.928
Infection: Parasite – Other2.0890.07913683.4455.452.244.981
Autonomic: Heart rate increase after standing1.9460.05810621.9350.444.644.9145
Comorbid: Inflammatory bowel disease2.0960.07815575.5554.151.645162
Immune: Chronic Sinusitis1.9690.0569423.87549.444.94580
Neuroendocrine Manifestations: Paraesthesia (tingling burning of skin)2.1770.07515722.6757.352.545.1129
Immune Manifestations: Hair loss2.1110.07517633.8955.253.545.1218
Onset: 1990-20002.1320.05630905.8356.246.345.142
Post-exertional malaise: Physically drained or sick after mild activity2.0920.06311092.955.347.145.1207
Neurological-Sleep: Prolonged Sleep1.9220.0599645.78448.141.645.237
Official Diagnosis: Autism20.08111715.0350.252.345.2207
Age: 50-602.0130.04916092.0250.43745.4142
Official Diagnosis: Chronic Fatigue Syndrome (CFS/ME)2.0460.05213112.6352.840.945.6528
Post-exertional malaise: Muscle fatigue after mild physical activity2.0870.06912312.775450.145.6265
Autonomic Manifestations: Orthostatic intolerance2.0870.06914092.7454.949.745.7164
Comorbid: Fibromyalgia2.0990.07418779.2255.953.246107
Neurological: Myoclonic jerks or seizures1.9820.05311801.649.936.94650
Official Diagnosis: Depression2.1370.06913752.195750.94699
Autonomic Manifestations: bladder dysfunction1.9470.06410480.6350.343.646.156
Official Diagnosis: Fibromyalgia2.0420.07120205.9953.150.846.173
Age: 40-501.9890.07310590.2650.352.146.2216
Joint: Tenderness2.1410.07419366.0656.451.846.2173
Gender: Male2.0660.06714723.2353.54946.2507
Post-exertional malaise: Physically tired after minimum exercise2.0530.06413813.9652.747.546.2268
Post-exertional malaise: Worsening of symptoms after mild physical activity2.10.06212504.3554.646.646.4282
Immune Manifestations: High Altitude Intolerance1.9970.06727233.951.54846.549
Official Diagnosis: High Blood Pressure (Hypertension)2.1490.07924512.0456.762.846.627
Comorbid: High Anxiety2.0850.0661647254.347.446.6302
Blood Type: O Positive2.1070.06114366.5654.843.446.7262
Autonomic: Inability to tolerate an upright position2.1190.07416184.9456.350.247136
Official Diagnosis: Autoimmune Disease2.2170.06918238.2359.449.847.3184
Comorbid: Methylation issues (MTHFR)2.1580.06611514.3557.85247.3113
Comorbid: Restless Leg2.0710.06510681.7354.548.847.493
Official Diagnosis: Mood Disorders2.2940.07410430.1762.857.747.654
Immune Manifestations: Inflammation (General)2.0870.07116527.1754.151.947.6277
Onset: less than 32 years since onset2.0530.06312146.1451.752.747.670
Neurological: Dysautonomia2.0250.06714155.1151.846.947.8156
Age: 30-402.0580.06611989.1553.149.948330
DePaul University Fatigue Questionnaire : Feeling like you have a temperature1.9380.07410889.8847.355.348.243
DePaul University Fatigue Questionnaire : New trouble with math2.190.07211232.0354.957.648.435
DePaul University Fatigue Questionnaire : Chilled or shivery1.9310.07126909.2646.450.948.647
DePaul University Fatigue Questionnaire : Sweating hands1.8590.09110413.7442.255.848.927
Official Diagnosis: COVID19 (Long Hauler)1.6170.08310288.0133.554.348.9203
Comorbid-Mouth: Mouth Sores2.1460.06617904.745545.648.970
Comorbid-Mouth: Ulcers (mouth)1.9640.06211296.4149.645.94927
Official Diagnosis: Osteoporosis1.8880.05410854.1447.140.84921
Immune: Viral infections with prolonged recovery periods2.0660.06611620.8553.648.84999
Comorbid: Salicylate sensitive1.5290.04810532.9230.137.549.136
Comorbid: Mood Swings1.990.0711071.2348.651.549.497
DePaul University Fatigue Questionnaire : Tingling feeling1.7050.07214165.0937.149.149.466
Blood Type: O Negative1.9450.07711344.3347.745.449.530
Comorbid: Electromagnetic Sensitivity (EMF)2.2240.06512963.0860.247.649.539
Neurological-Sleep: Sleep Reversal2.2250.06510837.6760.153.249.633
Neuroendocrine Manifestations: Painful menstrual periods2.1450.05911232.2157.645.449.657
DePaul University Fatigue Questionnaire : Impaired Memory & concentration2.0370.06917173.9851.449.349.7298
Comorbid: Carbohydrate intolerance1.9610.06112491.8951.145.349.946
DePaul University Fatigue Questionnaire : Frequently get words or numbers in the wrong order2.0950.07712878.055354.649.956
DePaul University Fatigue Questionnaire : Chest pain1.9660.07813689.9347.955.450.327
Onset: 1980-19902.0430.04737107.5653.836.750.432
DePaul University Fatigue Questionnaire : Poor Appetite1.9490.05414012.9248.543.750.537
Official Diagnosis: Attention deficit hyperactivity disorder (ADHD)2.0810.07811843.4955.154.850.580
Comorbid-Mouth: Periradicular periodontitis inflammatory / chronic lesion around roots of teeth2.0310.04811195.2454.438.950.625
DePaul University Fatigue Questionnaire : Nausea1.8560.0741235344.351.850.763
Physical: Eastern European1.710.05711299.2136.845.950.834
DePaul University Fatigue Questionnaire : Difficulty reasoning things out1.9550.07811585.794852.950.979
Joint: Redness2.2740.07222181.7261.8505146
DePaul University Fatigue Questionnaire : Blurred Vision1.7660.06211329.2439.445.95162
DePaul University Fatigue Questionnaire : Difficulty falling asleep2.0240.0812073.250.153.851133
DePaul University Fatigue Questionnaire : Unrefreshing Sleep, that is waking up feeling tired2.0620.06816938.435248.951.4334
DePaul University Fatigue Questionnaire : Racing heart1.9530.07522527.5546.751.551.467
DePaul University Fatigue Questionnaire : Feel unsteady on feet2.0260.05713562.4650.137.951.941
DePaul University Fatigue Questionnaire : Fatigue2.0930.06716345.9753.248.852.1380
DePaul University Fatigue Questionnaire : Muscle Pain (i.e., sensations of pain or aching in your muscles. This does not include weakness or pain in other areas such as joints)1.9680.07220265.447.353.152.2117
General: Heavy feeling in arms and legs2.0660.06612763.2253.348.952.3104
DePaul University Fatigue Questionnaire : Upset stomach1.8390.0721705.8242.847.552.379
DePaul University Fatigue Questionnaire : Weight change2.0060.06711665.4550.450.452.560
DePaul University Fatigue Questionnaire : Pain in Multiple Joints without Swelling or Redness1.9460.0615796.9546.649.352.574
Autism: More Inappropriate Social Interaction2.0860.08611929.5454.154.152.624
Comorbid: Constipation and Diarrohea (not explosions)1.9570.06312512.6748.74852.798
Comorbid: Sleep Apnea Diagnosis2.0540.05941891.1952.747.852.747
DePaul University Fatigue Questionnaire : Difficulty retaining information2.0280.06618395.9350.848.653134
DePaul University Fatigue Questionnaire : Mood swings2.140.07312088.4453.352.253.281
DePaul University Fatigue Questionnaire : Shortness of breath2.0310.07212631.2749.147.853.271
DePaul University Fatigue Questionnaire : Difficulty recalling information1.980.06717335.974949.553.2152
DePaul University Fatigue Questionnaire : Eye pain1.8810.05116658.3343.142.953.360
DePaul University Fatigue Questionnaire : Headaches1.9380.07721075.746.751.753.397
Physical: Long term antibiotics(over 6 months)1.9530.08213398.7847.462.553.332
Comorbid: Migraine2.070.07218043.7151.250.553.490
DePaul University Fatigue Questionnaire : Sore Throat1.9640.06814178.0448.445.353.557
Physical: Long term (chronic) stress1.8490.0619406.0543.246.153.5102
DePaul University Fatigue Questionnaire : Forgetting what you are trying to say2.0390.06918515.8150.351.453.6122
DePaul University Fatigue Questionnaire : Night sweats2.0380.06812137.1749.147.153.846
DePaul University Fatigue Questionnaire : Frequently loose train of thought2.1050.07912781.1553.757.353.8107
DePaul University Fatigue Questionnaire : Difficulty following things1.9950.0813048.194953.95489
DePaul University Fatigue Questionnaire : Depression2.0690.06519883.2752.749.75499
DePaul University Fatigue Questionnaire : Allergies1.9210.05912296.6547.245.554141
DePaul University Fatigue Questionnaire : Difficulty comprehending Information1.9720.08312479.6747.754.454.1121
DePaul University Fatigue Questionnaire : Abdomen pain1.9580.07422318.1248.25354.278
DePaul University Fatigue Questionnaire : Hot or Cold spells1.9350.06523234.8847.445.454.268
Blood Type: A Positive2.1670.07816858.155.65354.2112
DePaul University Fatigue Questionnaire : Muscle weakness1.9580.06612329.447.849.454.2123
DePaul University Fatigue Questionnaire : Sensitivity to Alcohol2.0560.06516243.851.646.254.398
DePaul University Fatigue Questionnaire : Difficulty finding the right word2.0310.06917169.1450.849.854.4181
DePaul University Fatigue Questionnaire : Does physical activity make you feel worse2.040.05917569.7851.447.254.5160
Physical: Steps Per Day 2000-40001.8980.05712403.945.541.954.769
Physical: Northern European1.8470.06213131.3143.244.954.7116
DePaul University Fatigue Questionnaire : Temperature lower than normal2.050.0613048.2450.344.854.863
Comorbid: Sugars cause sleep or cognitive issues1.9880.07114434.5651.954.854.832
DePaul University Fatigue Questionnaire : Difficulty staying asleep2.1350.06518877.495448.854.9141
Age: 0-102.0830.11614335.8955.462.654.987
Official Diagnosis: Celiac Disease2.0360.0820864.1551.154.95534
Condition: Acne1.9260.05518545.0447.345.155.180
DePaul University Fatigue Questionnaire : Walking up early in the morning (e.g. 3AM)2.1360.0621152.254.347.755.1102
Autism: More deficits in Language Comprehension2.1180.09312237.6955.860.255.135
DePaul University Fatigue Questionnaire : Confusion/disorientation1.9050.07512532.1745.753.755.160
DePaul University Fatigue Questionnaire : Need to nap during each day1.8690.06525116.6244.847.655.385
DePaul University Fatigue Questionnaire : Trouble expressing thoughts2.0480.07912709.9150.55655.391
Autism: More Decrease in Speaking1.9560.08911878.7849.852.455.441
DePaul University Fatigue Questionnaire : Tense muscles1.8840.06521790.0345.646.955.581
DePaul University Fatigue Questionnaire : Post-exertional malaise, feeling worse after doing activities that require either physical or mental exertion2.0440.06413295.6550.949.355.5191
Condition: Non-alcoholic Fatty Liver Disease1.9270.07112291.7648.44955.729
DePaul University Fatigue Questionnaire : Rash2.1410.0712809.34564955.941
Condition: Post-Traumatic Stress Disorder2.0730.0661317252.151.456.161
Autism: More Avoidance of Eye Contact or Poor Eye Contact1.9540.08714132.0849.952.456.226
Condition: ME/CFS with IBS1.9410.06421176.4347.646.656.2146
DePaul University Fatigue Questionnaire : Absent-mindedness2.0060.0719498.3149.65256.2119
Autism: More Behavioral Disturbances2.3810.10513815.9166.763.956.323
Condition: ME/CFS without IBS1.9840.06212510.5849.145.956.489
Physical: Paleo Diet1.7680.03812820.7440.531.556.523
DePaul University Fatigue Questionnaire : Slowness of thought1.9410.0712898.6346.849.456.6104
DePaul University Fatigue Questionnaire : Abnormal sensitivity to light2.0140.0691415448.949.356.7102
Official Diagnosis: Gastroesophageal reflux disease (GERD)2.0150.05719077.851.744.856.765
Autism: More Sleep Disturbances2.1360.08413719.1456.255.956.836
Physical: Good Air Quality1.7150.05512224.2137.642.956.829
DePaul University Fatigue Questionnaire : Need to have to focus on one thing at a time1.9490.06113809.3948.245.656.8120
Physical: Steps Per Day 4000-80001.9130.06612897.5845.547.15760
Autism: More Repetitive Movements2.0380.10512658.4853.662.35729
DePaul University Fatigue Questionnaire : Ringing in the Ears1.9980.06220337.648.447.557.2126
DePaul University Fatigue Questionnaire : Dizziness1.9830.06614162.5746.548.557.365
DePaul University Fatigue Questionnaire : Chemical sensitivity2.2210.06614833.7257.148.557.379
DePaul University Fatigue Questionnaire : Anxiety/tension2.0370.06718111.3151.449.257.5159
Autism: More Intense Focus on One Topic2.3550.05915148.7763.747.757.522
Physical: Tonsils removed2.0770.06913512.9254.645.457.749
General: Anhedonia (inability to feel pleasure)1.9830.06916245.0747.554.157.827
DePaul University Fatigue Questionnaire : Poor hand to eye coodination2.3290.0714096.3857.252.15821
Condition: Psoriasis2.1740.0826532.5256.854.458.233
Neuroendocrine Manifestations: Poor gut motility1.8880.06719063.3144.148.458.3133
DePaul University Fatigue Questionnaire : Concern with driving2.0840.05313892.6553.343.158.340
DePaul University Fatigue Questionnaire : Easily irritated2.0770.0715797.3552.651.358.4142
Physical: Work-Sitting1.9240.06218699.6446.145.258.5139
Physical: Breastfed2.170.04916236.9354.141.158.873
Neurocognitive: Aphantasia ( inability to visualize mental images)1.9390.07814582.4647.757.458.826
Official Diagnosis: Hypercholesterolemia (High Cholesterol)2.0340.06313217.8850.94859.240
Condition: Non-Celiac Gluten Sensitivity2.0190.05713551.5450.244.859.478
DePaul University Fatigue Questionnaire : Slow to react2.1130.0714951.9352.751.259.475
Condition: Asthma2.2020.07114193.3156.955.259.532
Physical: Steps Per Day 8000-160002.180.06319185.9555.547.860.137
Immune Manifestations: Chronic Flatus / Flatulence / gas2.0580.0712241352.449.460.298
Physical: Amalgam fillings2.1080.05529287.5954.239.960.449
Condition: Generalized anxiety disorder2.1830.0773906157.554.760.545
Physical: Appendix removed2.1590.05219123.7155.64260.828
Physical: Pets2.1220.06824978.4653.645.760.890
DePaul University Fatigue Questionnaire : Does physical activity make you feel better1.9090.0720720.1647.451.961.338
Autism: High Functioning2.3830.06115824.1466.946.561.342
Physical: Steps Per Day < 20001.9980.05616104.5249.742.561.563
Comorbid: Panic Attacks2.1940.07332169.335750.362.348
Official Diagnosis: COVID19 (Fully Recovered)2.090.05815757.6752.447.162.427
Condition: Osteoarthritis1.8920.05714280.8748.64463.123
Physical: Organic Diet2.1310.07126542.3153.64663.565
Immune Manifestations: Hyperphagia (abnormally hunger or desire to eat)2.010.05114582.6749.943.563.721

Objective evidence — the smart watch dimension

People who have read my blogs over the last few decades know that I keep to direct evidence; I avoid speculation and “I figure things work this way” thinking. Microbiome tests is a key part of it. My preference is to get as much data as is affordable/reasonable. This is typically my Bacteria Reported/Cost ratio. At the moment, Thorne is the distinctive winner.

Another data source can be smart watches. I have written about this in the past, Monitoring watch for CFS and other Conditions [2021]. After two years, my watch suffered failure on the charging toggle; so time to get a new one — what I got is described below. Every year features increases on smart watches. My first watch took only a few measurements and only on the hour.

Not Prestige Watches

I could go Apple Watch ($400), Fitbit ($300), Samsung ($450) etc. and drop a few hundred dollars for a device that will likely be technologically obsolete in 2 years. Or go with a Chinese model that costs $40 and which will last 2 years or more. In many cases, the key sensors may be the same as used in the prestige models. In some cases, these Chinese watches have features not available on the prestige watches.

Accuracy/Medical Grade is NOT the purpose

I use the watch to detect differences. In general, I find the results are reasonably accurate when I compare to standalone devices.

For most people (especially those with brain fog), their memory is poor and often they do not feel there was any change based on subjective memory. Having daily history going back months allows you to get objective measurements of things that change. Hopefully, it will stop you from ceasing something that is actually helping. Remember, I am very objective evidence based.

Review of my latest watch

You can find them on Temu or Banggoods. My model is E500. Once I got mine, my wife wanted to upgrade to the same model and did.

The screens

How many steps today and hours of sleep with details below

Then Heart Rate, BP and ECG (manually done)

Some Drill Down Details

Sleep Quality is often influenced by the Microbiome

Having daily detail breakdown is sweet!

The heart rate also maps activities (such as steps) providing better understanding!

With a good summary

Blood Pressure is every 5 minutes. With the other data, if there is a spike, you have enough other measurement to evaluate the events and causes.

Oxygen Measurement is far better than a finger device!

And more details

HRV – Heart Rate Variability

With simple summary and ratings

Below is an example from a day that I was pushing myself for physical activity more than usual (some who use the term “out of shape”). Fatigue was definitely happening!

Night Sweats

At present, I do have night sweats — the temperature monitor definitely show it. They start about 3 hours after going to bed and stops when I wake. As is common for people with ME/CFS (including those that are recovered), I have below normal temperatures.

Blood Glucose Levels

This can be very good to determine how well your meals are handled by your body

Bottom Line — Concrete, Detailed Objective Data!

There is a little overhead. I usually do periodic screen captures on my phone and off load the images to my PC so I can compare what was to what is.

Mast Cells and Bifidobacteria

This study Microbial patterns in patients with histamine intolerance. Journal of physiology and pharmacology : an official journal of the Polish Physiological Society 2018 reports low Bifidobacteriaceae (NCBI:31953). The Artificial Intelligence Algorithms on Microbiome Prescription (and most medical professionals) would suggest Bifidobacterium probiotics as a possible treatment. Unfortunately, very few medical professionals outside of Poland would have read the above study!

I decided to look at the literature to see if the AI suggestions have been validated by actual studies. This is a few of the studies that I found (the ones where the title alone is sufficient):

Bottom Line

Bifidobacterium Longum appears to be the best researched and easily available as a single species. Different species of probiotics can cause a different response — so keep to single species probiotics and avoid probiotic mixtures as a general rule. My personal favorite source is Custom Probiotics (no financial interest), they are:

  • by far the cheapest per BCFU,
  • his recommended daily dosages are at therapeutic levels (80- 320 BCFU per day)
  • his recommended method of taking is, IMHO, the correct way: NOT IN CAPSULES, but in a glass of water so it impacts the entire system from the mouth downwards (see 24 Years of ME/CFS with Mouth Microbiome for more information and studies)

Watch out for shooting yourself in the Microbiome!

Often I have encounter people frustrated over their inability to increase bifidobacterium or Lactobacillus. When they disclose what they are also taking — it becomes apparent why!

Going to Details about Bifidobacterium: NCBI 1678 we see what increases or decrease it. You may wish to consider reducing or eliminating these items.

General SubstanceSpecific SubstanceEffect
Herb or Spiceascophyllum nodosum (sea weed)Studies report Decreases in consensus
Herb or SpiceberberineStudies report Decreases in consensus
Herb or SpiceCurcuminStudies report Decreases in consensus
Herb or Spicegalla chinensis (herb)Studies report Decreases in consensus
Herb or Spicegarlic (allium sativum)Studies report Decreases in consensus
For Herbs
General SubstanceSpecific SubstanceEffect
Amino Acid and similarLeonurineStudies report Decreases in consensus
Amino Acid and similarmelatonin supplementStudies report Decreases in consensus
General SubstanceSpecific SubstanceEffect
Diet Styleanimal-based dietStudies report Decreases in consensus
Diet Stylegluten-free dietStudies report Decreases in consensus
Diet Stylehigh beef dietStudies report Decreases in consensus
Diet Stylehigh-fat dietsStudies report Decreases in consensus
Diet Stylehigh-protein dietStudies report Decreases in consensus
Diet Stylehigh-saturated fat dietStudies report Decreases in consensus
Diet Stylelacto-ovo-vegetarian dietStudies report Decreases in consensus
Diet Stylelow carbohydrate dietStudies report Decreases in consensus
Diet Stylelow fodmap dietStudies report Decreases in consensus
Diet Stylelow-fat dietsStudies report Decreases in consensus
Diet Stylemagnesium-deficient dietStudies report Decreases in consensus
Diet types
General SubstanceSpecific SubstanceEffect
Vitamins, Minerals and similarFerric citrateStudies report Decreases in consensus
Vitamins, Minerals and similarfluorine (i.e. tooth paste)Studies report Decreases in consensus
Vitamins, Minerals and similarfolic acid,(supplement Vitamin B9)Studies report Decreases in consensus
Vitamins, Minerals and similarpyridoxine hydrochloride (vitamin B6)Studies report Decreases in consensus
Vitamins, Minerals and similarretinoic acid,(Vitamin A derivative)Studies report Decreases in consensus
Vitamins, Minerals and similarthiamine hydrochloride (vitamin B1)Studies report Decreases in consensus
Vitamins, Minerals and similarVitamin B-12Studies report Decreases in consensus
Vitamins, Minerals and similarvitamin b3 (niacin)Studies report Decreases in consensus
Vitamins, Minerals and similarvitamin b7 biotin (supplement) (vitamin B7)Studies report Decreases in consensus
Vitamins, Minerals and similarVitamin C (ascorbic acid)Studies report Decreases in

The beef/protein diet are high in B-vitamins – thus very logical that both groups decreases.

Microba Reports usefulness has dropped!

A reader email me informing me that Microba no longer supplies 4 files, just one — Species. So no Phylum, Family or Genus information. I have modified the upload to handle just having one file available for whatever usefulness is possible.

A Long Time Pain

Microba does not provide data with the official NCBI Taxon numbers (which is what drives Microbiome Prescription AI). This means having to do name match over 3,635,527 different names on the NCBI database. Unfortunately, we still do not find matches, a few examples:

  • Pauljensenia MIC9711
  • QAMI01 MIC9451
  • Ruminiclostridium_C sp000435295
  • UBA1191 MIC6579
  • UBA1191 MIC9444

Getting more information usually result in this from Google:

I have written them in the past hoping they would be more willing to cooperate. No luck.

What is Available

When you look at the microbiome tree, you will see values only for species. Everything else is 0. It is impossible to accurately estimate genus etc from species alone.

Prior, we would see something like this:

And you will get nothing from Dr. Jason Hawrelak Recommendations. Only one species is in it.

On the positive side, you will still get reasonably accurate KEGG based data (since that is based on species).

“Just Give Me Suggestions” will still work to some extent. Other suggestions can be tricky. The AI will work to the extent of the data available (which is greatly reduced compared to Thorne, Ombre or Biomesight).

Bottom Line

For those people in Australia, I would suggest moving over to BiomeSight, you will likely get six times more data at a lower cost.

High Tick-borne Bacteria Counts

A reader wrote:

How does having Ehrlichia and Rickettsia in high values in the sample correspond to having these Lyme coinfections systemically? These are fairly common to see in the sample but my values are very high 96 and 99%.

From a reader

What is he talking about?

Ehrlichia is a genus of Rickettsiales bacteria that are transmitted to vertebrates by ticks. These bacteria cause the disease ehrlichiosis, which is considered zoonotic, because the main reservoirs for the disease are animals… Originally called Rickettsia ruminantium, and is currently named Ehrlichia ruminantium[Wikipeadia]

Rickettsia is the name of a single genus, …Many new strains or species of Rickettsia are described each year… Some Rickettsia species are pathogens of medical and veterinary interest, but many Rickettsia are non-pathogenic to vertebrates, including humans[Wikipedia]

He mentions they are common to see, let us look at the upload stats. From Ehrlichia: NCBI 943

And looking at Rickettsia: NCBI 780

The microbiome raises Yellow Flags only

For both of the above, the species or strains you have may be non-pathogenic (or even you are not susceptible to them). There are two steps that should be considered:

  • Do you have any symptoms for either condition?
  • If you have symptoms — then take the microbiome results to your MD quickly and ask for further testing (the above pages enumerates the appropriate tests)
  • If you do not have any symptoms, then for your next regular appointment, mention this — your MD may or may not do tests. Typically some symptoms is needed to justify the testing cost to insurance.

Is the Microbiome a Leading or Trailing Indicator?

A leading indicator is one that has the microbiome shifting before the diagnosis is usually done. This could be viewed as the microbiome shift feeding the condition. A trailing indicator means that the condition develop and then the microbiome changes.

We so not know the answer. I tend to favor it being a leading indicator, thus, when the shifts are towards a known condition then you can take action and either slow the progression or prevent it. Since the main mechanism (diet change) is extremely safe and usually very affordable — it appears to be rational.

24 Years of ME/CFS with Mouth Microbiome

Back Story

My history is:

  • currently 56 years old
  • CFS started at age 32 after a bad cold
  • I’ve had bloating and burping since hospitalized as a child for a lump on my throat. I received antibiotics at this time
  • I went into 80% remission for about 6 years from age 50-56. I don’t know what did it but I was on a low FODMAPS diet and started using hydrogen peroxide as a mouth rinse
  • Symptoms
    • in addition to the bloating and burping I have the following symptoms
    • fatigue
    • sometimes a numb feeling in parts of my hands and feet
    • orthostatic intolerance (although I did the tilt table test and tested negative)
    • halitosis
    • tinnitus
    • a strange feeling in my head
    • shortness of breath

I took inulin before my remission and my symptoms intensified immensely (especially burping and fatigue and shortness of breath)

I had a culture of my upper duodenum done in 2013 and it showed 10000CFU/ml of rothia, prevotella melaninogenica and streptococci viridins. A recent Bristle Health oral biome test showed the prevotella melaninogenica in the 90th percentile


I was not surprised about getting ME/CFS after a cold. Cold virus include COVID which can cause Long COVID — a sibling of ME/CFS. The wrong cold virus combined with other catalysts can send someone down that path.

First, I look at the distribution of percentiles. A normal/typical microbiome should have the same count (percentage) in each of the 10%ile. As is often seen with ME/CFS and Long COVID, we have a major overrepresentation of the 0-9%ile — 4x the count of most other groups.

0 – 96289
10 – 191422
20 – 291522
30 – 391616
40 – 491519
50 – 592025
60 – 691014
70 – 791822
80 – 892017
90 – 992135

I interpret this as a host, “a mafia”, of odd bacteria that cross support each other and pumps disrupting metabolites (chemicals) into the body. Thus it is not a bacteria(person) that causes the problems but a big gang of bacteria.

There was not a strong bacteria that predominate this shift, Phocaeicola massiliensis was the only candidate. Looking at Potential Medical Conditions Detected, there were no significant matches (not surprising with an abundance of low percentile bacteria).

Bacteria deemed unhealthy is a pretty long list.

Looking at Dr. Jason Hawrelak Recommendations, we see several that are usually low percentiles that are too too low. These include: Bifidobacterium, Lactobacillus, Methanobrevibacter, Roseburia and Faecalibacterium prausnitzii.

TaxonomyRankLowHighYour ValueStatus
Bacteroidiaclass03537.564Not Ideal
Akkermansiagenus133.225Not Ideal
Bacteroidesgenus02029.183Not Ideal
Bifidobacteriumgenus2.550.015Not Ideal
Lactobacillusgenus0.0110.002Not Ideal
Methanobrevibactergenus0.00010.020Not Ideal
Roseburiagenus5101.154Not Ideal
Bilophila wadsworthiaspecies00.250.575Not Ideal
Escherichia colispecies00.010.006Ideal
Faecalibacterium prausnitziispecies10155.159Not Ideal

Looking at some of the conditions we see a marginally better match for Long COVID than for ME/CFS! Not sufficient to ascribe to a cold virus as the onset cause, but interesting.

  • Long COVID   (62 %ile) 16 of 204
  • Chronic Fatigue Syndrome   (60 %ile) 4 of 64

Going over to our special studies, we see Long COVID is the best match

Bristle Health Results

This is the first time that I have seen this report. It is a mouth test from (good name, better then ToothBrushHealth!). I have pointed out the importance of the mouth in prior posts: A mouth full – for better or worst [2014] and Your mouth can trigger flares[2017].

It provides information on selected strains by role:

As an exercise to understand the “end-to-end” process (literally), I have created the table below. Since the data is by species we have an issue of different tests reporting different species. For more details see The taxonomy nightmare before Christmas… The * indicate that there was no match at the strain level, so we use the genus as a proxy.

First thing to remember is that bacteria is pH sensitive so the quantity in each location is expected to be very different.

Actinomyces dentalis1.890*
Actinomyces graevenitzii1.990*
Actinomyces odontolyticus0.490*
Atopobium parvulum6.869*
Atopobium sp869*
Campylobacter concisus5.298*
Campylobacter gracilis5.198*
Candida albicans1.8
Candida dubliniensis1.5
Candida glabrata2.2
Candida sp1.1
Capnocytophaga granulosa7.3
Capnocytophaga sputigena0.19*
Capnocytophaga sp0.18*
Corynebacterium matruchotii8.386*
Dialister micraerophilus0.494*
Eikenella corrodens2.6
Enterobacter cloacae2.5
Fusobacterium nucleatum1.919
Fusobacterium sp0.392
Gemella haemolysans1.848*
Gemella morbillorum0.1248*
Granulicatella adiacens (30%)4.815
Haemophilus haemolyticus4.8
Haemophilus parainfluenzae7.2
Haemophilus pittmaniae0.79
Helicobacter pylori2.361*
Lactobacillus fermentum3.55*
Leptotrichia trevisanii0.99
Megasphera micronuciformis8.524*
Neisseria elongata0.15*
Neisseria flavescens2.1
Neisseria mucosa3
Neisseria subflava1
Oribacterium sp0.09826
Porphyromonas sp2100
Porphyromonas catoniae0.27100*
Prevotella sp1073
Prevotella fusca2.273*
Prevotella histolica9.573*
Prevotella loescheii1.61
Prevotella melaninogenica973*
Prevotella pallens0.173*
Prevotella salivae8.873*
Prevotella tannerae0.5673*
Prevotella veroalis7.573*
Propionibacterium acidifaciens2.1
Rothia aeria0.8
Rothia mucilaginosa5.2
Selenomonas noxia4.472*
Solobacterium moorei0.389
Stomatobaculum longum0.18 
Streptococcus constellatus2.748*
Streptococcus infantis7.948*
Streptococcus intermedius1.90
Streptococcus mitis7.848*
Streptococcus oralis7.21
Streptococcus parasanguinis1.349
Streptococcus peroris1.648*
Streptococcus salivarius548*
Streptococcus sanguinis248*
Streptococcus tigurinus8.748*
Tannerella sp0.88
Treponema sp0.73
Veillonella atypica8.518
Veillonella dispar7.518*
Veillonella sp2.718*

I noticed something interesting with strains that were in both samples.

My subjective conclusion is that this strongly supports the hypothesis that the mouth microbiome feeds the microbiome of the rest of the digestive track. We have 4 rare strains in the above list of 7 where only 1 would be expected to be below 14% (1 in 7).

We can get suggestions for the mouth approximately by using this feature and entering by the genus items above 7 for high, 9 for very high or below 3 for low, below 1 for very low.

All Bacteria [Genus] Reported720 Bacteria

Suggestions include (for mouth) are below. This is an experiment to see how suggestions for the “other end” compares! Values below 0.4 are usually low significance.

There are some subjective issues in entering the contents and getting suggestions. For suggestions, doing parent and/or children can be debated many ways. Some species are low of a genus and others are high… do you mark the genus high, low or normal? It is unclear if the bacteria listed are pure bad or just bad in excess. That is, should anything not zero be deemed too high or only those over 7. Things are not sufficiently cleared from this report. If I get more requests to do analysis of Bristol Health reports, I will invest more time and add a custom manual entry page. I will need to research every single species to know the appropriate handling.

Below is for purposes of illustration only

Avoids include: xylan (prebiotic), lactobacillus plantarum (probiotics)berberine, Cacao, d-ribose

Microbiome Suggestions

The adage “No man can server two master” is good to keep in mind in this scenario.

I did the usual “Just Give Me Suggestions” path since there was nothing that stood out that could require special handling. “Just Give Me Suggestions” obtains 4 sets of suggestions using different logic to try to derive the best suggestions. I will start by taking the above list and see how they rank in terms of the microbiome.

Modifier (Alt Names on Hover)Mouth
🕮  inulin (prebiotic)1  📏-27
walnuts0.863  📏6
whole grain diet0.588-14
🕮  lactobacillus reuteri (probiotics)0.471  📏34
rare meat0.3925.6
refined wheat breads0.392126
triphala0.392  📏-10
Slippery Elm0.39249.8

As expected, with my two masters preamble, we have disagreements. All of the mouth items came in as weak suggestions against BiomeSight suggestions (range: -460 to 465), so doing them will likely not have significant impact on the other end’s microbiome.

Back to Microbiome Suggestions, we have in decreasing priority (excluding antibiotics):

And on the to avoid

Looking at Diet Styles, only two are strong indicated, both avoids (listed above).

Food Site

The food site takes the nutrients found and assists in building a food menu plan.

👍86.67Vitamin B-12
👍84.71Vitamin C
The top Nutrients Suggested

For the top one, a nutrient unfamiliar to most people, we see this list to choose from. We See Barley on it. It Barley is a problem, then almond, peanut or pistachio are good alternatives. For Peanuts, I actually did some posts in the ME/CFS context.

mg per 100 gramsFood

Similarly, Naringin points to Grapefruit (just about the only choice) with rosmarinus officinalis (rosemary) being a vert diminished next choice.

Thiamin is an easy to find vitamin — Vitamin B1

Hesperetin is in Lime, Blond Orange, Lemon and Grapefruit (AGAIN Grapefruit!)


Q: What testing method is BristleHealth using?

A: “Shotgun microbiome test examples: Bristle (oral microbiome).” [src] Biomesight is using 16s which provides less data. Thorne uses shotgun testing and thus would be a better match.

Q: On cfsremission and/or cort johnsons blog you discussed the importance of breaking down biofilms with things like nac as well as rotating herbs, probiotics and antibiotics. Is that a layer that should be added onto the items selected by microbiomeprescription (I plan to reread those posts before starting).

A: Yes, I have posted about biofilm in the past: Combating an Infection Defense Mechanism: Biofilms [2014] and Probiotic Biofilm Breakers[2016]. It is not a simple matter “Biofilms provide survival sites for both beneficial and opportunistic pathogenic bacteria, by providing protection as above and increasing the potential of the bacteria to survive and evolve” [2013]. It impacts antibiotic resistance [2020]. In other words, we have yin-yang. If you are intending to aggressively reduce bacteria known to use biofilms, especially with antibiotics, then it is a wise choice. In most cases, I would not do it by default. For example, Akkermansia muciniphila and Lactobacillus rhamnosus GG both form biofilms [2020].

Q: What can you suggest to deal with Halitosis (Bad Breath)

A: The bacteria involved are nicely listed in your report.

We will again use All Bacteria [Genus] Reported but deem all of the above to be high (0-5), very high (5+).

In the resulting list we see many items that can be used as teas (which would likely impact the mouth bacteria): triphala, oregano (origanum vulgare, oil) . Items that can be chewed in the mouth: mastic gum .

On the avoid: alcoholic beverages (rarely an option with ME/CFS), gluten-free diet, aspartame (sweetener).

The same approach may be done for other mouth bacteria that you wish to eliminate, you should cross check that none of the substance are strong avoid for the “other end”.

More Readings:

Bottom Line

This person’s microbiome matches the pattern usually seen with ME/CFS and Long COVID. The suggestions are also in general keeping with what has been reported to reduce symptoms. The B-Vitamins are well established. Some other citations, Brain “fog,” inflammation and obesity: key aspects of neuropsychiatric disorders improved by luteolin [2015], Modulation of antigen-induced chronic fatigue in mouse model of water immersion stress by naringin, a polyphenolic antioxidant [2009]

The oral microbiome impacting the entire flow (including SIBO) seems to be well illustrated with this data. The bacteria strains from the Bristle Health report appear to be those known to cause issues in the mouth (and most are not reported on by other tests). This implies that the ideal pair of tests to deal with systemic health issue is likely Bristle Health and Thorne.

Exploration into grass allergies

Allergies are often tossed into a big box of “all allergies are the same”. I have learnt from studies that often different items are clustered together to avoid needing to learn and detail with the details. I know people that have very specific allergies — i.e. to birch but not grass or other tree pollens. Most MDs will toss such people in the seasonal allergic rhinitis bucket; treating them proforma.

This appears borne out by some studies:

  • ” A delayed correlation between the birch pollen concentration and the symptom scores was seen up to two days after the pollen measurement. For grass pollen this effect lasted up to three days after the pollen measurement.”[2023]
  • “the most effective treatments for allergic rhinitis were in order as follows: sublingual immunotherapy_dust mite, subcutaneous immunotherapy_dust mite, sublingual immunotherapy_ grass mix plus pollen extract, placebo, and pharmacotherapy. ” [2023] – note that placebo was more effective that traditional medicine!

The goal of this exercise is see if there are any new options or approaches for addressing this issue.

Environment May Be a Factor

Some of my university professors refused to believe that allergic rhinitis existed. They were born and raised in a part of the middle east and never encountered people with it before moving to North America. This saying from the prophet recorded by Salamah b. al-Akwa, implies that allergies may have been unknown in that part of the world:

When a man sneezed beside the prophet (May peace be upon him), he said to him : Allah have mercy on you, but when he sneezed again, he said : The man has a cold in the head.

This seen in the following charts: (A) Unspecified rhinitis; (B) allergic rhinitis; (C) non‐allergic rhinitis.

Worldwide prevalence of rhinitis in adults: A review of definitions and temporal evolution [2022]

Treatment Trends

Things here gets a little complex…

B cells are key players in the mechanisms underlying allergic sensitization, allergic reactions, and tolerance to allergens. Allergen-specific immune responses are initiated when peptide:MHCII complexes on dendritic cells are recognized by antigen-specific receptors on T cells followed by interactions between costimulatory molecules on the surfaces of B and T cells. In the presence of IL-4, such T-B cell interactions result in clonal expansion and isotype class-switching to IgE in B cells, which will further differentiate into either memory B cells or PCs. Allergic reactions are then triggered upon cross-linking of IgE-FcɛRI complexes on basophils and mast cells, leading to cell degranulation and the release of pro-inflammatory mediators.Mechanisms underlying effective allergen-specific immunotherapy (AIT) involve the induction of Tregs and the secretion of blocking IgG4 antibodies, which together mediate the onset and maintenance of immune tolerance towards non-hazardous environmental antigens. 

B Cell Functions in the Development of Type I Allergy and Induction of Immune Tolerance [2022]
  • Oralair, a biologic, has grown in use in Europe (approved in 2008 from 8% to 29% by 2012 [2015]) and is approved in the USA (2013) Link to FDA documents. It is prescription with a base cost of $5 or more per tablet — hence, antihistamines are more likely to be recommended in the US due to cost, not effectivity.
  • Similar items are also available, (2800 BAU grass SLIT-T) [Relative to placebo, grass AIT treatment improved total combined scores by 20% 2011], Grazax [The active group demonstrated a 31% reduction in median rhinoconjunctivitis symptom [2011]], MK-7243. There are not cures, rather reduces severity for a percentage of people.

“The only treatment available to treat grass allergy is immunotherapy treatment. This is when you are exposed to small but increasing doses of allergens over a long period of time to help stop your allergic reaction. It takes a long time to work and needs to be prescribed by an allergy specialist.” Australian Department of Health

Treatment via Microbiome

For grass allergy we have the following available retail with studies which boils down to 2 probiotic species worth considering.

Lactobacillus casei ShirotaYakultOral delivery of Lactobacillus casei Shirota modifies allergen-induced immune responses in allergic rhinitis. [“ Volunteers treated with LcS showed a significant reduction in levels of antigen-induced IL-5, IL-6 and IFN-gamma production compared with volunteers supplemented with placebo. Meanwhile, levels of specific IgG increased and IgE decreased in the probiotic group.”]
Lactobacillus rhamnosus GGCulturelle®Effect of Lactobacillus rhamnosus GG and vitamin D supplementation on the immunologic effectiveness of grass-specific sublingual immunotherapy in children with allergy. [“Reduction in the symptom-medication score and improvement in lung function as well as a significant increase in the percentage of ….in all the groups were observed compared with control group”]
Lactobacillus rhamnosus GR-1RepHresh™ Pro-B™ ProbioticDevelopment and pilot evaluation of a novel probiotic mixture for the management of seasonal allergic rhinitis. [“provided few clinical benefits.”]
Mutaflor (Escherichia coli strain Nissle 1917)Mutaflor (Canada, Australia, Findland, Germany)Tolerability and clinical outcome of coseasonal treatment with Escherichia coli strain Nissle 1917 in grass pollen-allergic subjects. [“not sufficient to achieve clinical efficacy in grass pollen”]
Strain Specific Probiotics

Non-Strain probiotic candidates:

  • Bifidobacterium longum [2023], lowers IgE (see below)
  • Lacticaseibacillus paracasei [2023] ” 2 billion CFU/day for 3 months ameliorated sneezing”

And this delightful title “Role of Probiotics in Patients with Allergic Rhinitis: A Systematic Review of Systematic Reviews” [2022] found no hard evidence for any specific probiotics.

Bottom Line for Probiotics: It seems that they need to be taken well in advance of allergy season with sufficiently large dosages.


I took the list of 1135 bacteria that produces nitric oxide and then looked at the 40 bacteria reported on National Library of Medicine Citations for Allergic Rhinitis (Hay Fever). I was disappointed not to find many matches. What I found were matches for:

  • Bacteroides (NCBI:816 )
  • Clostridium (NCBI:1485 )
  • Acidaminococcus intestini (NCBI:187327 )

Next, I went to samples that are annotated with Official Diagnosis: Allergic Rhinitis (Hay Fever) – about 200 samples, and then cross apply them to the above 1135 bacteria. There are no strong statistical significance found.

Haemophilus parainfluenzae56.141
Pelosinus fermentans60.122
Limosilactobacillus fermentum
a.k.a. Lactobacillus fermentum
Veillonella atypica52.922
Veillonella dispar52.749
Ombre Labs

How to do this experiment

  • Go to your samples
  • Look at Microbiome Tree
  • Search for the items above
  • Hand pick (if you have any matches)

This exploration failed to produce any significant finding or insights. 🙁

Exploring Immunoglobulin (IgE etc)

As a starting point, Immediate Hypersensitivity Reactions [2023] is of special interest for those who have reactions within 24 hours. “Antibodies including IgE, IgM, and IgG mediate them… Allergic rhinitis is another atopic disease where histamine and leukotrienes are responsible for rhinorrhea, sneezing, and nasal obstruction. ” Typically only IgE is involved. IgE increase in response to grass pollen exposure and are responsible for the allergic symptoms.

  • “Patients with pollen allergy but not control donors have a population of circulating allergen-specific B cells with the phenotype and functional properties of adaptive memory B-cell responses. These cells could provide precursors for allergen-specific IgE production upon allergen re-exposure.” [2015] – which implies repeat exposure may increase severity.
  • Omalizumab: reduced significant clinical exacerbation within 24 weeks [2023]

FYI On Other Allergies

Mast Cells Issues can be moderated by some Bifidobacterium bacteria (Click for studies).

Bottom Line

Symptom relief via antihistamines or DAO for a subset for immediate response, or months of preparation for allergy season by probiotics and biologics.

DAO levels were lower in AR patients compared with the controls. The DAO level did not significantly correlate with the severity of AR according to the Allergic Rhinitis and its Impact on Asthma (ARIA) score, though it was lower in patients with persistent or moderate to severe symptoms. The total IgE, eosinophil percentage, and SNOT-22 score all had an inverse relationship with DAO.

Predictive Value of the Serum Diamine Oxidase Level in the Diagnosis of Seasonal Allergic Rhinitis [2022]”

Avoidance of Grass Pollen

This is really what the Asthma and Allergy Foundation of America strongly advocates.

Above memory B-cell responses were cited in research which I translate that repeated exposure will make it worse, hence one approach is aggressive avoidance.

  • Wearing a N95 or better mask when outside from the start of pollen season onwards. In some cases a full face mask may be better. When you arrive home, do a complete change of clothes as soon as possible (ideally outside) and take a shower.
  • Aggressively reduce pollen in your living place (i.e. pollen leaking into the house via windows and open doors)

Our Approach

This household’s solution for grass allergy has been HEPA air filters oversized for the room size. For example, this $90 unit is rated for 183 sq ft. We would use it for 90 sq ft only — the size of a small bathroom (8′ x 10′). A 10x more expensive unit (Austin HEALTHMATE PLUS ) is rated for 1500 sq ft, so we will use it to cover only 750 sq feet. This means that a 2,000 sq ft house would need at least three operating. Note that this intentional oversizing is to reduce the time to remove grass pollen that comes in.

Time to Reduce Pollen from opening a door

The Austin does 400 cubic feet per minute and we can assume that for one complete room exchange that the pollen level will drop by 50%. It will not remove all in one room exchange. You remove 400 cf in a minute and shoves the clean air back into the room — diluting the air that is there. A little calculus finds that after one cycle, we are down 50% only.

Sample Calculation: 750 sq ft x 8 ft ceiling = 6000 cu feet … thus 15 minutes for one exchange with a 400 cfm unit (i.e. the Austin). If we go with manufacture specifications of 1500 sq feet, than 30 minutes to remove half of the pollen.

PPM, or pollen per cubic meter.

Consider a High Grass level at 340. After one room exchange, it would be 170 (still high), after two room exchanges it would be at 85 (still high), after three exchanges down to 43 – moderate, and at 4 exchanges we are at 20 — into the low range at last. In short, after opening a door for a short while, it may take 2 hours for the pollen level to get reduced to acceptable levels.

Conclusion: Keep the doors open for the least amount of time possible. Consider adding automatic door closers to all doors. Windows should not be open and they should be tight seals. A furnace that brings air in from the outside as part of normal operation should have HEPA filters installed on the intake.

We went one step further, we added to our house an air pump that takes air thru a HEPA filter and creates a positive air pressure in the house. This is one way to address leaky doors and windows — instead of pollen leaking in, the positive pressure pushes it away. We originally installed it to address wild fire smoke (works nicely), but this pollen season it has made a noticeable difference.

Is the cause of gluten sensitivity drinking water?

If you look at my 2018 post “What is the best diet in your opinion?” [repost in 2022], you will find a logic that is simple: your microbiome adapts over generations to the food available. When food choices quickly, issues arise in the microbiome. One known issues:

The other day I spotted a non-alcoholic Imperial Pale Ale at Costco and picked up a dozen. During the summer when I am working outside, I like having a cold one when I come inside. Health Canada in 2023 updated their guidance to restrict alcohol use to standard drinks or less per week  with discussion about putting health labels (like tobacco labels) on all drinks. This product tastes like a good IPA, but has no significant alcohol — likely close to the common beer that my ancestors had for breakfast, lunch and dinner.

The light went on! Up until around 1900, beer and ales were common daily drinks –including for children. The reason was simple, water was often deadly due to bacteria in it. Clean drinking water was scarce or unreliable. Milk was fine. Coffee and Tea was fine. Water was not. The beer was not the typical 8% alcohol often seen in American Beers, but 2% or less.

This leads to the speculation that removing regular gluten exposure during childhood — via weak beers and plain-old-school porridge (oats, barley etc.) is the cause of the exploding gluten sensitivity!

It is very likely that gluten sensitivity is connected to diet changes – most of our wheat was breed for specific things, like yield per acre — those changes may contribute too. It is impossible to find clear evidence — but blaming drinking water is an amusing suggestion!

When SIBO Treatment Fails

SIBO or Small Intestinal Bacterial Overgrowth was first proposed as a medical condition in 1970. The first use of breath tests for it was around 1974. The key things to remember is that this condition was the naming of a collection of symptoms. The name reflected the speculation on the general cause without any specifics. Over the years, this condition has been broken down in 6 general subsets depending on the results of breath test (and a potential 7th, if the symptoms are there but no positive breath test results).

Assuming that it is a bacteria overgrowth — which bacteria is overgrown? The breath test does not provide evidence on which specific bacteria a person has.

Based on Kyoto Encyclopedia of Genes and Genomes, we see many suspect bacteria. Worse still, it may not be a single species overgrowth but several.

  • Hydrogen Levels (H2) – 595 species
  • Methane Levels (CH4) – 622 species
  • hydrogen sulfide (H2S) – 3817 species

The clinical practice is often applying a simple logic “If it is an overgrowth, we just toss the appropriate antibiotic at it and it is solved!”. Experience has shown that some are generally effective, i.e.

  • Rifaximin was 78% effective [2023]
  • Amoxicillin (500 mg 3 times a day per, during the first month), followed by ciprofloxacin (500 mg twice a day per, during the second month) and metronidazole (500 mg 3 times a day per, during the third month) about 56% effective [2023]

With effective usually being defined as symptom improvement not remission. Reporting adverse reaction is poorly done.

The reality that using herbs, oil of.. , tinctures, etc. have the same problem as antibiotics. With the evidence above there is not way to determine which ones will be effective for the individual.

There is a recognized and accepted way to better determine the bacteria involved: Small Intestine Aspirate. This is a quasi-surgical procedure to take a sample from the Small Intestine.

Small-bowel aspiration during upper esophagogastroduodenoscopy: Rao technique [2020]

The gotcha is the handling of the sample, the treating physician or the lab may do one of several possible things:

  • Just report the quantity (confirming an overgrowth) — most common
  • Classic culturing of the sample — which will report on the culturable bacteria (most are NOT culturable)
  • 16s testing of the sample – better resolution
  • Shotgun testing of the sample — best resolution

Cost issues can be complicated by insurance companies not covering the costs in most situations.

The Downstream Proposal

Whatever is in the small bowel or intestine eventually makes it way thru the entire system and ends up in a stool. The amount will likely differ because of passages through multiple environments.

The motivation for this post was a reader telling me that his hydrogen sulfide levels have become a problem. His latest sample had a significant amount of them. This suggests that 16s sampling can be helpful for detecting the species involved and thus treatment suggestions based on the bacteria that appear to be in overgrowth (by virtue of the breath test elements).

The video below takes you through the process.

A Walkthru

Note that the top antibiotics suggested from Microbiome Prescription are those used for treating SIBO.

Suggested Readings

Many older articles have stale information, the following are very recent publications.